I've read that only about 50,000 SS folks were involved by war crimes. So that leaves a lot of folks who didn't get their hands dirty. And the guy in Berlin that had to track soap and toilet paper usage doesn't have the same culpability as a death camp commandant. As for the Godwins Law comment - it is comforting to try to think of Nazis as being uniquely evil, but most of them were just ordinary folks.
I can't speak for the state of the immortal souls of anyone. As C.S. Lewis said, whether you're positioned so that your anger sends millions to their deaths or simply causes folks in the office to laugh and make fun of you, the stain on the soul is the same.
Leaving that aside, it is ridiculous to compare a relatively powerless, mostly irrelevant and aging church of only 2 million (if that - that's THEIR number, which I know includes us even though we left 6 years ago) with a totalitarian national government that managed to murder 8-10 million people.